MmuINT0109815 @ mm10
Intron Retention
Gene
ENSMUSG00000038146 | Notch3
Description
notch 3 [Source:MGI Symbol;Acc:MGI:99460]
Coordinates
chr17:32133388-32135547:-
Coord C1 exon
chr17:32135385-32135547
Coord A exon
chr17:32133693-32135384
Coord C2 exon
chr17:32133388-32133692
Length
1692 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CACACTACTGGTTCCTGCAGATG
3' ss Score
8.63
Exon sequences
Seq C1 exon
GTAGAGGAGCCGGGCATGGGTGCAGAGGAGCCTGAGGACTGTCGCCAGTGGACCCAACACCACCTGGTTGCTGCTGATATCCGTGTGGCACCAGCCACAGCGCTGACTCCTCCTCAGGGAGATGCAGATGCAGACGGAGTGGATGTCAACGTCCGAGGGCCTG
Seq A exon
GTGAGTGCCCTCCCAAAGAGGCCCTCATTGGTCCTACCTGCTGGATCCCATGCAGGGGTTCTGGGAGCGTCTGGGCCTCTGGGCCTCTGGGCCTCTGGGCCTCTGGGCCTGCTGCGTGTGTTGTATTCTAAGTGATTGGAACGCCATGCAAGGTGAAGCAGAAGGTGGGCTGGCTGCAACTGAGAACCCTGAGGCTGTGTGGACCCTGGACTCTTTCTTTTATGAGATTAAAATTTCCTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTATTTTTCTTTTCTTTTTTTCTTTATTTTTTTCTTTTTTTGTTTTTCTTTTTTTAGATTTATTTATTATTATATCTAAGTACACTGTTGCTCTCCTCAGACACACCAGAAGAGGGTGTCAGATCTCATTATGAGTGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTTCAGAAGAGCAGTCAGTGCCCTTACCAGCTGAGCCATCTCACCAGCCCTCTCTTTTTGTTTTTCAAGACAGGGTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAAACCAAGCTGGCCTCTGAACTCTGAGATCCACCTGCCTCTGCCTCTTGAGTGCTGGGGTTGAAGGTGTTTGCTCCCCCAACCCCAGCTCTTTCTTCCTGTGTAGCCCTGGCTGTCCTGGAACTTACTCTGTAGACCAGGCTGGCTCCAAACCCATAGAGCTCCACTTACCTCATCCTCCCGAGTACTGGGATTAAAGGCTTGTTCCAGCACCACCACTGCCTGGCTCTTGCTCTTGCTCTTTCTCTCTTTCTCTCTTTCTCTCTTTCTCTCTTTCTCTCTTTCTTTCTCTTTCTCTTTCTTTCCCTTTCTTTCTCTCTCTCTCTCTCTTTCTCCTTCTTCTTCCTCCTCCTCTGCCTCCTCTTCCTCTTCCCTCTCCTCTTCTTCCTCTTCCTCTTCCTCCTCCTCTTTCTTGTTATACTTTTATATAAGATTTCACTATATAGCTCTGGCTATCCTGGAACTCATAATGTAGATCAAGTTGTTGTGAAGTCACAGAGATCCTCCTGCCTCTGTCCCCCAAGTGCTGGAATTAAATGTGTATGCCATCATATCCAGCTGGGATTTATTTAAAAATCACACTTATTTGTGTGTATTCGTGTACTCGGAAGTCAGAGGACACCTTACTGGAGTTGATTATCTCCTATCTCGGTCCAAGAGATCTCATTCACGCTGTCCAGTTTCTCTGTAGCTTCTCTATCCATCAAGCTCCTGGATGTTCAATCCCTCCTTACCCCTCTAGCCCCCTTAGCTTCAGCCATACAGCTTGTCAGGAGAGTCTCGGATTAGTTCTGACAGGGTGAACTAGAACCACGTACTTATTCCTGGGCCAATGAATGTGGCTAGGGCCTATAATATGCAGATAAGCCAGTCCCCATCTGGTCTAAGTAGGGCTTGCTATTAGGGAATTCGTGAGGAGAACTAGGGAAAAGGTGGTTCCCTTCCCCTTTATTCCAAGTGCTCGGCTTCCTGGAATCGCTTTTGCGGTCCATCATGTAATCTTCGTGGGGTGGCTTTGCAGTTGGGAGAATTTACCTCTGTCTGTGGCGCTGTGTGTCACAGTGCCCCTGACATTTGCCCCAGGAAGACCCCTATGCCTGTGACACACTACTGGTTCCTGCAG
Seq C2 exon
ATGGCTTCACCCCACTTATGCTGGCCTCCTTCTGTGGGGGAGCCCTGGAGCCGATGCCAGCTGAGGAGGATGAGGCGGATGACACATCAGCCAGCATTATCTCAGATCTGATCTGTCAAGGGGCCCAGCTCGGGGCACGGACTGACCGCACTGGCGAGACCGCCCTGCATTTGGCTGCCCGCTATGCTAGAGCGGATGCAGCCAAGCGTCTCCTGGATGCTGGGGCGGACACCAACGCCCAGGATCATTCGGGCCGCACCCCCCTGCACACCGCAGTGACAGCTGATGCCCAGGGTGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038146:ENSMUST00000087723:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.800 A=NA C2=0.373
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF127962=Ank_2=PU(83.7=75.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGGAGCCTGAGGACTGTC
R:
CTGCATCCGCTCTAGCATAGC
Band lengths:
342-2034
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types